Hello again,
Made a new scan with all boxes checked - and it came out with this result:
[Feb 20 20:10:24]Preparing a new scan.Done.
[Feb 20 20:10:24]Remote scan of public facing site only available to paid membersPaid Members Only
[Feb 20 20:10:26]Check if your site is being Spamvertized is for paid members onlyPaid Members Only
[Feb 20 20:10:28]Checking if your IP is generating spam is for paid members onlyPaid Members Only
[Feb 20 20:10:30]Scanning your site for the HeartBleed vulnerabilitySecure.
[Feb 20 20:10:37]Fetching core, theme and plugin file signatures from WordfenceSuccess.
[Feb 20 20:10:40]Fetching list of known malware files from WordfenceSuccess.
[Feb 20 20:10:42]Comparing core WordPress files against originals in repositorySecure.
[Feb 20 20:10:42]Comparing open source themes against WordPress.org originalsProblems found.
[Feb 20 20:10:42]Comparing plugins against WordPress.org originalsSecure.
[Feb 20 20:10:42]Scanning for known malware filesSecure.
[Feb 20 20:11:07]Scanning file contents for infections and vulnerabilitiesSecure.
[Feb 20 20:11:07]Scanning files for URLs in Google's Safe Browsing ListSecure.
[Feb 20 20:12:37]Scanning posts for URL's in Google's Safe Browsing ListSecure.
[Feb 20 20:12:38]Scanning comments for URL's in Google's Safe Browsing ListSecure.
[Feb 20 20:12:38]Scanning for weak passwordsSecure.
[Feb 20 20:12:38]Scanning DNS for unauthorized changesSecure.
[Feb 20 20:12:38]Scanning to check available disk spaceSecure.
[Feb 20 20:12:38]Scanning for old themes, plugins and core filesProblems found.
[Feb 20 20:12:38]Scan complete. You have 11 new issues to fix. See below.Scan Complete.
I have been through the discrepancies between the originals and the website files - and they are all changes made by me.